The owner of a Queensland aviation company is due to face court today, accused of organising a “black flight” to smuggle two alleged Australian fugitives to Indonesia.

The Australian Federal Police said its investigation began in November when Indonesian immigration officials detained two pilots and two passengers who arrived on a small fixed-wing plane at Merauke, in the Indonesian province of South Papua.

The flight’s certificate of clearance listed only the two copilots, one from Indonesia and one from Australia, the AFP said.

The other two undeclared passengers were from Sydney and wanted by NSW Police.

The 43-year-old owner of an aviation company, from Woolshed, west of Ipswich, is due to appear in the Ipswich Magistrates Court today, charged with two counts of people smuggling.

‘Network’ of charter flights

The AFP said investigators arrested the man on Wednesday after searching the man’s property in south-east Queensland and his business premises in Rockhampton.

AFP Detective Superintendent Adrian Telfer said police would allege the man had organised a sophisticated people smuggling operation.

Drone pic of tip of Cape York, the most northern point on the Australian mainland

The men left Australia on a “black flight” from Cape York Peninsula to Merauke in Indonesia. (ABC News: Brendan Mounter)

“We allege he coordinated a network of connected charter flights on different planes and with different companies over a week to smuggle the fugitives from New South Wales to north Queensland, then on to Indonesia,” he said.

One of the wanted men, aged 34, was on bail for kidnapping offences with conditions not to approach any point of interstate or international departure.

The other, 35, has three outstanding arrest warrants, including for supplying and manufacturing a commercial amount of drugs.

NSW Police said the relationship between the men was not known.

The wanted men remain in detention in Indonesia, and NSW Police said they would monitor the situation.

The men flew from Orange, in central west New South Wales, to Cape York on November 10 last year, Superintendent Telfer said.

They were allegedly driven or flown to various locations in Far North Queensland over the next week, before the “black flight” to Indonesia took place on November 17.

The plane’s transponder was allegedly deactivated before the men were picked up from a remote airstrip at Port Stewart on eastern Cape York.

The transponder was not turned back on until the plane was in international waters.

Police ‘reverse engineered’ travel

Investigators are still looking into how much the charter operator may have allegedly been paid to do the job, or whether he was coerced or threatened, Superintendent Telfer said.

“Based on the sophistication to get these fugitives out of Australia over the course of a week, with multiple flights, accommodation, we believe the figures are extensive,” he said.

“In terms of the motivation, that’s something we’re still exploring.”

The two pilots and the alleged fugitives remain in detention in Indonesia.

Superintendent Telfer said police had “essentially reverse-engineered their travel” after the plane landed in Indonesia.

He implored other air charter operators to contact police if they had been approached to run similar black flights.

“We have intelligence that there have been people who have exited Australia similar to this,” he said.